CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research

CottonGen (http://www.cottongen.org) is a curated web-based relational database providing a central repository and data-mining resource for genomics, genetics, and breeding data of cotton. CottonGen contains whole genome sequences and annotation of both G. raimondii and G. arboretum - the ancestors of tetraploid commercial cottons, the unigenes for the family and the genera, gene sequences from NCBI, genetic maps, trait loci, germplasm, marker diversity, breeding, and publication data. All predicted genes of the whole genome sequence, unigenes and NCBI genes have been further annotated by homology to genes in other species, InterPro protein domains, GO terms and KEGG pathway terms. Whole genome sequences and annotation including genes, mRNAs, markers, re-sequencing data, NCBI sequences and homologous genes from other species, can be viewed through GBrowse and JBrowse. Pathway data can also be accessed through the CottonCyc Pathways. New querying functionality includes an advanced marker search, gene search, publications search and a sequence retrieval tool. Data submission templates, tutorials and a frequently asked questions section have also been added. Future development will include implementation of a breeder’s toolbox, and addition of synteny, gene/genome curation tools as well as more map, marker and trait data.